comparison split_file_on_column.xml @ 5:d4b5b70e82cb draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit df81dd26ed1cf67a0d95b9614738b1d59667773f

4:37a53100b67e

<tool id="tp_split_on_column" name="Split file" version="0.4">
    <description>according to the values of a column</description>
    <requirements>
        <requirement type="package" version="5.0.1">gawk</requirement>
    </requirements>
    <command>
<![CDATA[

        awk -F'\t' '{print > "tmp_out/"\$$column".$infile.ext" }' '$infile'
    #end if
]]>
    </command>
    <inputs>
        <param format="tabular" name="infile" type="data" label="File to select" />
        <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />

        <param name="include_header" type="boolean" label="Include the header in all splitted files?"
               help="Include the first line (the assumed header line) in all splitted files." />
    </inputs>
    <outputs>
        <collection name="split_output" type="list" label="Table split on first column">
            <discover_datasets pattern="__name_and_ext__" directory="tmp_out" />
        </collection>
    </outputs>
    <tests>
        <test>

        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

This tool splits a file into different smaller files using a specific column.
It will work like the group tool, but every group is saved to its own file.
You have the option to include the header (first line) in all splitted files.
If you have a header and don't want keep it, please remove it before you use this tool.
For example with the "Remove beginning of a file" tool.

-----

**Example**

Splitting a file without header on column 5 from this::

    chr7  56632  56652  cluster 1
    chr7  56736  56756  cluster 1
    chr7  56761  56781  cluster 2
    chr7  56772  56792  cluster 2
    chr7  56775  56795  cluster 2

will produce 2 files with different clusters::

    chr7  56632  56652  cluster 1
    chr7  56736  56756  cluster 1


    chr7  56761  56781  cluster 2
    chr7  56772  56792  cluster 2
    chr7  56775  56795  cluster 2

]]>
    </help>
    <citations>
        <citation type="bibtex">

5:d4b5b70e82cb

<tool id="tp_split_on_column" name="Split by group" version="0.5">
    <requirements>
        <requirement type="package" version="5.0.1">gawk</requirement>
    </requirements>
    <command>
<![CDATA[

        awk -F'\t' '{print > "tmp_out/"\$$column".$infile.ext" }' '$infile'
    #end if
]]>
    </command>
    <inputs>
        <param format="tabular" name="infile" type="data" label="File to split" />
        <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />

        <param name="include_header" type="boolean" label="Include header in splits?"
               help="Include the first line (the assumed header line) to all split files." />
    </inputs>
    <outputs>
        <collection name="split_output" type="list" label="Split by group collection">
            <discover_datasets pattern="__name_and_ext__" directory="tmp_out" />
        </collection>
    </outputs>
    <tests>
        <test>

        </test>
    </tests>
    <help>
<![CDATA[

========
Synopsis
========

Given a single input dataset this tool splits the file on unique values from a specified column.

===========
Description
===========

This tool splits a file into a collection based on unique values of a speific column.
It performs a grouping operation with every group saved as a separate collection element.
You have the option to include the header (first line) to all splits.
If you have a header and don't want keep it, please remove it before you use this tool.
For example with the "Remove beginning of a file" tool.

-----

**Example**

Splitting this file on column 1::

    chr1 10 20
    chr1 30 40
    chr2 40 70
    chr4 60 80


will produce a collectiion with 4 elements::

    chr1 10 20
    chr1 30 40

    chr2 40 70

    chr4 60 80

------

.. image:: $PATH_TO_IMAGES/split_by_group.svg
  :width: 800
  :alt: Split by group

]]>
    </help>
    <citations>
        <citation type="bibtex">